Alfonso “Little Al” D’Arco, acting head of the Luchese crime family, was the first mob boss to turn government witness. He flipped for the feds in 1991 and helped send more than 50 mobsters to prison. Now in witness protection, D’Arco shared his story with reporters Jerry Capeci and Tom Robbins for their new book, “Mob Boss.” Here D’Arco reveals details of one of New York’s most storied pizzerias, Ray’s. While the name became famous, its real business wasn’t pepperoni and cheese — it was heroin.

In 1959, a lean, dark-haired young hoodlum from Little Italy named Ralph “Raffie” Cuomo was released from prison after serving a stretch for armed robbery. He’d been caught robbing a posh restaurant across the street from the Waldorf-Astoria. A shootout erupted. One of Cuomo’s pals was shot dead and a cop wounded. Cuomo took a pistol-whipping from police. His picture ran in the papers, blood streaming down his face, a patrolman tauntingly pointing a gun at his head.

But he served less than three years. Back home and looking for a new start, Cuomo opened a pizzeria on the ground floor of an old tenement at 27 Prince St., where he’d grown up. He used recipes his mother had brought from Italy. He called the place Ray’s Pizza. (He would later explain that “Ralph’s Pizza” sounded too “feminine.”) He was a good cook. He had a white pizza, no tomatoes, that drew crowds. The restaurant became popular, the name famous. But sauce and mozzarella were only a sideline.

The shop’s real trade was drugs.

The chef’s supply chain for narcotics came via a notorious family that lived around the corner on Elizabeth Street. The DiPalermo brothers were all leading members of the Luchese crime family, the Mafia borgata of which Little Al D’Arco would later become acting boss.

Oldest of the clan was Joseph “Joe Beck” DiPalermo, a short, wispy man with thick horn-rim glasses considered by law enforcement to be “the dean of the dope dealers.”

Younger brothers Charles “Charlie Brody” and Peter “Petey Beck” DiPalermo served as able assistants. After Charlie Brody married Raffie’s older sister, Marion, Cuomo was welcomed into the family business.

Al D’Arco had always been wary of Raffie Cuomo, considering him too wild to be trusted. Today, from witness protection, D’Arco recalled, “He was a stickup guy, taking chances on armed robberies.”

But the pizza parlor and its adjoining clubhouse soon became headquarters for “the Prince Street crew,” a prime gathering spot for local mobsters.

“Raffie went into business with Charlie Brody and the rest of the Becks moving heroin,” D’Arco said. “He became a big narcotics guy.”

There were a few business setbacks. In 1969, Cuomo was caught with $25 million worth of heroin in his car trunk. He served a few years, then went back to the pizzeria and started dealing all over again.

None of the Prince Street crew used drugs themselves. But they had another addiction that drove them to ever-larger heroin deals. “They were all degenerate gamblers. Each one of them. They would gamble a hundred thousand dollars, lose it, and then have to do another dope deal,” D’Arco revealed.

Most nights, Cuomo was somewhere laying down a bet. “He’d be at the racetrack three or four times a week, the Meadowlands. And he was at the casinos in Atlantic City all the time, didn’t matter how much he lost.”

He still had enough loot left over for side investments. The chef ran a sports-betting operation, specializing in weekly football sheets. He also loaned cash to those in need. “He was a shylock, he had a lot of money out on the street,” said D’Arco.

The drugs and the cash were handled in the pizzeria’s unfinished basement, directly beneath the ovens. “The place had whitewashed walls and like a dirt floor.” Tree trunks, polished but untrimmed and dating from the turn of the century, held up the floor joists.

“They had one of Joe Becky’s kids, Anthony, going over to the East River Savings Bank at Lafayette and Spring Street with bags of bills. They had a guy in the bank on their payroll who handled the money for them. They made millions in babania — heroin. All the brothers and Raffie did. That’s what they were all about. They never stopped dealing. They were at it night and day.”

They also tutored D’Arco in the trade. He tried several heroin deals with the crew, hoping to score some of the big money for himself. But he was less successful. One shipment was rejected by customers as worthless. Another buyer turned out to be a federal drug-enforcement agent. Arrested and convicted in 1983, he served three and a half years in prison.

When Al D’Arco got back to Little Italy, he found Raffie Cuomo and the Prince Street crew still flourishing. Only now their drugs were being sold locally, to neighborhood kids. Even two of Al’s children had become users.

D’Arco was irate. “I blamed the Prince Street crew, Petey Beck, his brothers, and all of them.”

He wasn’t the only one. Drugs had been sold out of a small Puerto Rican-owned bodega down the street from St. Patrick’s Old Cathedral School, the Catholic grade school on Prince and Mott streets.

“They were selling drugs out of that store and their own grandchildren were going to the school on the corner. This nun from the school went out and screamed at them, right in front of their club there on Prince Street.”

Al D’Arco wasn’t about to become a crusader. He was a gangster. Drugs sold and consumed elsewhere, he rationalized, had nothing to do with him. But the line had been crossed when his gangland pals had let it be peddled on their own streets.

Selling drugs was supposed to be against mob rules, a potential death penalty for violators. But that was mob make-believe, Al knew. Mafia members and crews broke the rule regularly, with apparent impunity. Leaders of his own Luchese crime family had been caught in massive drug schemes, without suffering any consequences. It was business, he figured. Making money.

But he hadn’t seen needles going into the arms of friends, or rent and food money going to feed the addictions of parents instead of their children. He’d been spared the robberies and break-ins afflicting neighborhoods where junkies did anything for a fix. That was someone else’s world. Not his own. Now it was in his own family, flowing into the veins of his own children.

“When I found out what was happening in the neighborhood, the first guy I grabbed was Petey Beck. And I took him to a luncheonette on the corner of Mott and Spring. I told him, broadly, like, ‘You know, if I ever get the f–king c–ksuckers pushing drugs through these Puerto Ricans in this neighborhood, I am going to kill every f–king one of them.”

Mob protocol prohibited D’Arco from accusing DiPalermo, but the mobster got the point. “He was a made guy. A captain. I wasn’t going to say nothing direct at him. Him and his brothers and Raffie, because of all their gambling and need for money, were pushing it to the kids. How could you do that?”

The warning had little effect. A few weeks later, Cuomo called Al into the club next to the pizza parlor.

“Raffie tells me he has four kilos of heroin to sell. I didn’t scream at him. He was a made guy, too, just like me. I just looked at him and said I wasn’t interested. That I was on parole and couldn’t take the chance.”

Meanwhile, Ray’s Pizza was a bigger hit than ever, the name now synonymous with the city’s best pies. Cuomo briefly branched out, opening another Ray’s on the Upper East Side, but he soon sold it. Others rushed to capitalize on the connection, each claiming to be the original. There was Famous Ray’s in Greenwich Village, Original Ray’s Pizza on First Avenue, a One and Only Famous Ray’s in Midtown, even a chain with parlors around the country.

At one point, Cuomo tried to cut himself into the profits from the fad he’d launched, seeking to trademark his now-celebrated name. A complicated legal battle ensued, and he dropped it. But when reporters came knocking on Prince Street to ask what he thought about what he’d started, Raffie Cuomo, an apron tied around a growing paunch, scoffed at the pretenders. “Their pizzas give us a bad name,” he said. “There’s nothing like our ‘Ray’s.’ ”

He shyly refused to pose for photos. He had no interest in having his picture in the papers again. What he also didn’t say was that competition didn’t really worry him. He was doing just fine with drugs. Often, he didn’t even bother to hide it.

One day, D’Arco watched with surprise as Cuomo bolted out of the pizzeria to his Cadillac parked in the lot next door. “He says, ‘I gotta make a delivery,’ and runs out.” But he wasn’t delivering pizzas. “He pops the trunk, pulls out a bag with a couple of kilos and walks right into the street with it. Then he jumps in another car and takes off.” The pie man returned an hour later, acting as if nothing had happened.

It was no mystery to law enforcement what was going on at the heralded pizzeria. But proving it was another matter. Three times, the Manhattan District Attorney’s Office planted bugs inside the pizza parlor and on the street outside in hopes of catching Cuomo and his pals in the act. It was close, but no cigar.

Wiretap affidavits submitted to court by DA Robert Morgenthau during a one-year-long probe in 1989 stated there was “reasonable cause to believe” that Cuomo, D’Arco and other Luchese crime-family associates were “committing the crimes of criminal sale of a controlled substance.”

On a late February night that year, investigators watched as Cuomo put a white shopping bag — filled with narcotics, they believed — in the trunk of his car and invited D’Arco and a fellow Luchese mobster over to look.

Detectives saw D’Arco reach inside the trunk, then lick his fingers. It was “a gesture that indicates the ‘tasting’ of narcotics,” prosecutors claimed in a court affidavit. But this time, they were wrong, D’Arco said. “Nah, that wasn’t dope. That was food. Raffie made a big tray of sausage and peppers. That’s what I was tasting. It was delicious.”

When he wasn’t cooking up heroin deals, Cuomo still liked to work in his kitchen. D’Arco, who was justly proud of the fare at his own nearby restaurant, La Donna Rosa, regularly stopped by Ray’s for a bowl of Italian soup — pasta e fagioli. “Every Wednesday, he’d make this pasta fazool. It was the best I ever had, I gotta give it to him.”

D’Arco told the FBI that story and many others when he broke with the Mafia in the fall of 1991 after learning that his Luchese-family bosses were plotting to kill him. A couple of years later, another Luchese defector who had carried out multiple major heroin deals with Cuomo provided even more details.

In October 1995, drug-enforcement agents arrested the Ray’s Pizza founder, charging him with operating a vast narcotics network from New York’s most famous pizzeria.

Cuomo delayed the inevitable for several years, finally cutting a favorable deal, agreeing to serve four years. At sentencing, his attorney made a last-ditch effort to reduce the term further, arguing that prison stress could kill his 62-year-old client, who was ailing from heart disease, diabetes and recent back surgery. Prosecutors pointed out that the pizza artist seemed to be in decent shape. He’d spent the previous night betting at the Meadowlands.

He survived that third prison term, returning to Prince Street after doing his time to oversee his still popular restaurant. That’s where he was in April 2008, when complications from the diabetes and the heart ailment did him in. Services were held across the street at Old St. Patrick’s Cathedral. Three years later, Ray’s sold its last pies when Cuomo’s family shuttered the landmark pizzeria.

As things turned out, the real estate was almost as profitable as the drug sales. In 2011, Cuomo’s heirs sold the five-story tenement at 27 Prince St. with the old tree trunks in the basement.

The price tag: $5.9 million.

Adapted from “Mob Boss: The Life of Little Al D’Arco, the Man Who Brought Down the Mafia” by Jerry Capeci and Tom Robbins. Out Oct. 1 from St. Martin’s Press.